how does mim-tRNAseq handle partially mapped tRNA sequence?

[lkong888]

Hi, thanks for this great tool for tRNA analysis. I wonder how does mim-tRNAseq handle partially mapped tRNA fragment? And does mim-tRNAseq count pre-tRNA as mature tRNA? In the case of pre-tRNA, there will be either tailer or header sequence. Will mim-tRNAseq clip those extra sequence and then consider it aligned? Or would it just discard those reads with extra leader or tailer sequence?